PWFSLSmoke v1.2.100

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Utilities for Working with Air Quality Monitoring Data

Utilities for working with air quality monitoring data with a focus on small particulates (PM2.5) generated by wildfire smoke. Functions are provided for downloading available data from the United States 'EPA' <https://www.epa.gov/outdoor-air-quality-data> and it's 'AirNow' air quality site <https://www.airnow.gov>. Additional sources of PM2.5 data made accessible by the package include: 'AIRSIS' (password protected) <https://www.oceaneering.com/data-management/> and 'WRCC' <https://wrcc.dri.edu/cgi-bin/smoke.pl>. Data compilations are provided by 'PWFSL' <https://www.fs.fed.us/pnw/pwfsl/>.

Readme


title: "PWFSLSmoke"

pagetitle: PWFSLSmoke"

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PWFSLSmoke R Package

Utilities for Working with PM2.5 Air Quality Monitoring Data

Background

The USFS Pacific Wildland Fire Sciences Lab AirFire team works to model wildland fire emissions and has created the BlueSky Modeling Framework. This system integrates a wide collection of models along a smoke modeling pipeline (fire information, fuel loadings, consumption modeling, emissions modeling, time rate of emissions modeling, plume height estimations, and smoke trajectory and dispersion modeling). The resulting model output has been integrated into many different smoke prediction systems and scientific modeling efforts.

The PWFSLSmoke R package is being developed for PWFSL to help modelers and scientists more easily work with PM2.5 data from monitoring locations across North America.

The package makes it easier to obtain data, perform analyses and generate reports. It includes functionality to:

  • download and easily work with regulatory PM2.5 data from the EPA and AirNow
  • download and quality control raw monitoring data from AIRSIS and WRCC
  • convert between UTC and local timezones
  • apply various algorithms to the data (nowcast, rolling means, aggregation, etc.)
  • provide interactive timeseries and maps through RStudio’s Viewer pane
  • create a variety of publication ready maps and timeseries plots

Installation

This package is designed to be used with R (>= 3.3) and RStudio so make sure you have those installed first.

Users will want to install the devtools package to have access to the latest version of the package from Github.

The following packages should be installed by typing the following at the RStudio console:

# Note that vignettes require knitr and rmarkdown
install.packages('knitr')
install.packages('rmarkdown')
install.packages('MazamaSpatialUtils')
devtools::install_github('MazamaScience/PWFSLSmoke', build_vignettes=TRUE)

Any work with spatial data, e.g. assigning countries, states and timezones, will require installation of required spatial datasets. To get these datasets you should type the following at the RStudio console:

library(MazamaSpatialUtils)
dir.create('~/Data/Spatial', recursive=TRUE)
setSpatialDataDir('~/Data/Spatial')
installSpatialData()

Examples

Additional R Notebooks that demonstrate the functionality of the package can be found in the localNotebooks directory on github. These notebooks are not part of the package because they require installation of the MazamaSpatialUtils datasets.

To run them you should:

  • make sure you have the proper spatial data installed in ~/Data/Spatial/
  • make sure you have both the knitr and rmarkdown packages installed
  • download the localNotebooks/ directory
  • open a notebook with RStudio
  • click the "Knit" or "Preview" button in RStudio

This R package was created by Mazama Science and is being funded by the USFS Pacific Wildland Fire Sciences Lab.

Functions in PWFSLSmoke

Name Description
addGoogleAddress Add address information to a dataframe
addEsriAddress Add address information to a dataframe
addWindBarb Add wind barb to a map
addUSGSElevation Add Elevation Data to a Dataframe
addClustering Add clustering information to a dataframe
addBullseye Add a Bullseyes to a Map or RgoogleMap Plot
AQI Official Air Quality Index Levels, Names and Colors
addMazamaMetadata Add State, Country and Timezone to a Dataframe
addPolygon Add a Colored Polygon to a Plot
addAQIStackedBar Create Stacked AQI Bar
airnow_loadAnnual Load annual AirNow monitoring data
airsis_BAM1020QualityControl Apply Quality Control to raw AIRSIS BAM1020 dataframe
airsis_createMonitorObject Obain AIRSIS data and create ws_monitor object
airsis_createRawDataframe Obain AIRSIS data and parse into a raw tibble
addGoogleElevation Add Elevation Data to a Dataframe
addShadedNight Add Nighttime Shading to a Plot
addAQILines Add AQI Lines to a Plot
addAQILegend Add an AQI Legend to a Map
addShadedBackground Add Shaded Background to a Plot
airnow_loadLatest Load most recent AirNow monitoring data
addWindBarbs Add wind barbs to a map
airsis_EBAMQualityControl Apply Quality Control to raw AIRSIS EBAM tibble
aqiColors Generate AQI Colors
airnow_loadDaily Load recent AirNow monitoring data
airnow_qualityControl Apply Quality Control to AirNow dataframe
airnow_createDataDataframes Return reshaped dataframes of AirNow data
epa_parseData Parse EPA data
aqiPalette Color Palettes for Air Quality Monitoring Data
createEmptyMetaDataframe Create Empty Site Location Metadata Dataframe
epa_createMonitorObject Download and convert hourly EPA air quality data
createEmptyMonitor Create empty monitor object
epa_downloadData Download EPA air quality data
airsis_createDataDataframe Create AIRSIS data dataframe
airsis_loadDaily Load recent AIRSIS monitoring data
airsis_createMetaDataframe Create AIRSIS site location metadata dataframe
airnow_downloadSites Download AirNow Site Location Metadata
airsis_ESAMQualityControl Apply Quality Control to raw AIRSIS E-Sampler dataframe
airsis_loadLatest Load most recent AIRSIS monitoring data
airnow_load Load Processed AirNow Monitoring Data
airsis_identifyMonitorType Identify AIRSIS monitor type
airsis_downloadData Download AIRSIS data
distance Calculate distances between points
airsis_availableUnits Get AIRSIS available unit identifiers
loadDaily Load Recent PM2.5 Monitoring Data
epa_load Load Processed EPA Monitoring Data
loadDataFile Load data from URL or local file
epa_loadAnnual Load annual EPA monitoring data
downloadDataFile Download data from URL to local diredctory
monitor_dailyThreshold Calculate Daily Counts of Values At or Above a Threshold
monitor_distance Calculate distances from monitors to a location of interest
airsis_parseData Parse AIRSIS data string
airsis_qualityControl Apply Quality Control to raw AIRSIS dataframe
googleApiKey API Key used for Google Geocoding Requests
initializeMazamaSpatialUtils Initialize Mazama Spatial Utils
esriToken Token used for ESRI Geocoding Requests
monitor_getCurrentStatus Get current status of monitors
monitor_dygraph Create Interactive Time Series Plot
monitor_downloadLatest Download recent PM2.5 monitoring data
monitor_extractDataFrame Extract dataframes from ws_monitor objects
monitor_getDailyMean Calculate daily means for a ws_monitor object
airnow_createMetaDataframes Create dataframes of AirNow site location metadata
monitor_downloadDaily Download recent PM2.5 monitoring data
monitor_downloadAnnual Download annual PM2.5 monitoring data
addIcon Add Icons to a Map or RgoogleMap Plot
addMarker Add Icons to a Map or RgoogleMap Plot
loadLatest Load Recent PM2.5 Monitoring Data
monitor_hourlyBarplot Create Hourly Barplot
epa_createMetaDataframe Create dataframe of EPA site location metadata
epa_createDataDataframe Create EPA data dataframe
monitor_rollingMean Calculate Rolling Means
monitor_rollingMeanPlot Create Rolling Mean Plot
parseDatetime Parse Datetime Strings
monitor_loadAnnual Load annual PM2.5 monitoring data
monitor_writeCurrentStatusGeoJSON Write current monitor data to geojson file
monitor_load Load PM2.5 monitoring data
monitor_join Merge Data for Monitors with Shared monitorIDs
monitor_combine Combine List of ws_monitor Objects into Single ws_monitor Object
monitor_loadDaily Load recent PM2.5 monitoring data
monitor_aqi Calculate hourly NowCast-based AQI values
monitor_dailyBarplot Create Daily Barplot
monitor_asDataframe Return Monitor Data in a Single Dataframe
airnow_downloadHourlyData Download hourly data from AirNow
airnow_downloadParseData Download and aggregate multiple hourly data files from AirNow
airnow_createMonitorObjects Obain AirNow data and create ws_monitor objects
monitor_collapse Collapse a ws_monitor Object into a ws_monitor Object with a Single Monitor
monitor_loadLatest Load most recent PM2.5 monitoring data
monitor_isEmpty Test for an Empty ws_monitor Object
monitor_staticmap Create a static map of ws_monitor object
monitor_nowcast Apply Nowcast Algorithm to ws_monitor Object
monitor_performance Calculate Monitor Prediction Performance
monitor_leaflet Leaflet interactive map of monitoring stations
monitor_subsetData Subset ws_monitor Object 'data' Dataframe
monitor_map Static map of monitoring stations
monitor_noDataPlot Create Blank Plot with "No Data" Message
monitor_isMonitor Test for an correct structure of ws_monitor Object
monitor_subset Subset ws_monitor Object
airsis_load Load Processed AIRSIS Monitoring Data
airsis_loadAnnual Load annual AIRSIS monitoring data
generic_parseData Parse generic air quality files
generic_downloadData Download generic data
monitor_scaleData Scale ws_monitor Data
getEsriToken Get ESRI Token
monitor_timeAverage Calculate Time Averages
monitor_timeInfo Get time related information for a monitor
skill_ROC ROC Curve
monitor_replaceData Replace ws_monitor Data with Another Value
monitor_trim Trim ws_monitor Time Axis to Remove NA Periods From Beginning and End
setGoogleApiKey Set Google API Key
monitor_reorder Reorder a ws_monitor bject
monitor_writeCSV Write monitor data as CSV
rawPlot_timeOfDaySpaghetti Create Time of Day Spaghetti Plot from a Raw Dataframe
rawPlot_timeseries Create Timeseries Plot from a Raw Dataframe
raw_getHighlightDates Return Day Stamps for Values Above a Threshold
wrcc_EBAMQualityControl Apply Quality Control to raw WRCC EBAM tibble
upgradeMeta_v1.0 Upgrade ws_monitor Metadata to Version 1.0
setEsriToken Set ESRI Token
skill_confusionMatrix Confusion Matrix Statistics
skill_ROCPlot ROC Plot
wrcc_createMonitorObject Obtain WRCC data and create ws_monitor object
wrcc_createMetaDataframe Create WRCC site location metadata dataframe
monitor_subsetMeta Subset ws_monitor Object 'meta' Dataframe
monitor_stamenmap Create a static map of ws_monitor object
staticmap_getEsrimapBrick Create a rasterBrick from an Esri tiled image server
staticmap_getRasterBrick Create a rasterBrick from a tiled image server
getGoogleApiKey Get Google API Key
staticmap_plotRasterBrick Plot an RGB rasterBrick
staticmap_getStamenmapBrick Create a rasterBrick from stamenmap tiles
wrcc_ESAMQualityControl Apply Quality Control to raw WRCC E-Sampler tibble
wrcc_createDataDataframe Create WRCC data dataframe
monitor_dailyStatistic Calculate daily statistics
monitor_dailyStatisticList Calculate Daily Statistics
monitor_isTidy Check if data is tidy-formatted ws_monitor data
%>% Pipe operator
monitor_isolate Isolate Individual Monitors
monitor_performanceMap Create map of monitor prediction performance
wrcc_createRawDataframe Obtain WRCC data and parse into a tibble
wrcc_downloadData Download WRCC data
monitor_toTidy Convert `ws_monitor` data to a tidy format
monitor_subsetByDistance Subset ws_monitor Object by Distance from Target Location
monitor_subsetBy Subset ws_monitor Object with a Filter
monitor_timeseriesPlot Create Timeseries Plot
monitor_print Print monitor data as CSV
rawPlot_windRose Create Wind Rose Plot from a Raw Dataframe
rawPlot_pollutionRose Create Pollution Rose Plot from a Raw Dataframe
wrcc_loadAnnual Load annual WRCC monitoring data
raw_enhance Process Raw Monitoring Data to Create raw_enhance Object
wrcc_loadLatest Load most recent WRCC monitoring data
wrcc_loadDaily Load recent WRCC monitoring data
wrcc_parseData Parse WRCC data string
tidy_toMonitor Convert `ws_tidy` data to a `ws_monitor` object
wrcc_identifyMonitorType Identify WRCC monitor type
timeInfo Get time related information
wrcc_load Load Processed WRCC Monitoring Data
wrcc_qualityControl Apply Quality Control to raw WRCC tibble
AQI_es Official Air Quality Index Levels, Names and Colors
PWFSLSmoke-deprecated Deprecated functions in PWFSLSmoke
US_52 US State Codes
AIRSIS AIRSIS Unit Types
CONUS CONUS State Codes
WRCC WRCC Monitor Names and Unit IDs
Northwest_Megafires Northwest Megafires Example Dataset
AQI_en Official Air Quality Index Levels, Names and Colors
Carmel_Valley Carmel Valley Example Dataset
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Vignettes of PWFSLSmoke

Name
Data_Model.Rmd
Maps_and_Timeseries_Plots.Rmd
NowCast.Rmd
PWFSLSmoke.Rmd
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